null Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vjv-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:56 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 318 and 0 Target number of residues in the AU: 318 Target solvent content: 0.6033 Checking the provided sequence file Detected sequence length: 415 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 415 Adjusted target solvent content: 0.48 Input MTZ file: 1vjv-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 49.299 81.862 107.491 90.000 90.000 90.000 Input sequence file: 1vjv-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3320 target number of atoms Had to go as low as 0.55 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 65.126 3.600 Wilson plot Bfac: 53.59 5232 reflections ( 96.71 % complete ) and 0 restraints for refining 3669 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.2932 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2918 (Rfree = 0.000) for 3669 atoms. Found 23 (23 requested) and removed 51 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 3689 seeds are put forward Round 1: 176 peptides, 31 chains. Longest chain 10 peptides. Score 0.384 Round 2: 212 peptides, 30 chains. Longest chain 21 peptides. Score 0.524 Round 3: 204 peptides, 30 chains. Longest chain 21 peptides. Score 0.498 Round 4: 227 peptides, 32 chains. Longest chain 22 peptides. Score 0.543 Round 5: 237 peptides, 32 chains. Longest chain 26 peptides. Score 0.572 Taking the results from Round 5 Chains 32, Residues 205, Estimated correctness of the model 3.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5232 reflections ( 96.71 % complete ) and 6877 restraints for refining 3008 atoms. 6089 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2403 (Rfree = 0.000) for 3008 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 2: After refmac, R = 0.2230 (Rfree = 0.000) for 2914 atoms. Found 15 (19 requested) and removed 14 (9 requested) atoms. Cycle 3: After refmac, R = 0.2317 (Rfree = 0.000) for 2879 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 4: After refmac, R = 0.1997 (Rfree = 0.000) for 2865 atoms. Found 14 (18 requested) and removed 16 (9 requested) atoms. Cycle 5: After refmac, R = 0.2051 (Rfree = 0.000) for 2848 atoms. Found 7 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 2950 seeds are put forward Round 1: 204 peptides, 35 chains. Longest chain 27 peptides. Score 0.424 Round 2: 217 peptides, 32 chains. Longest chain 24 peptides. Score 0.512 Round 3: 228 peptides, 33 chains. Longest chain 22 peptides. Score 0.532 Round 4: 216 peptides, 29 chains. Longest chain 18 peptides. Score 0.550 Round 5: 229 peptides, 31 chains. Longest chain 21 peptides. Score 0.562 Taking the results from Round 5 Chains 31, Residues 198, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5232 reflections ( 96.71 % complete ) and 6446 restraints for refining 2840 atoms. 5670 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2288 (Rfree = 0.000) for 2840 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 7: After refmac, R = 0.1998 (Rfree = 0.000) for 2797 atoms. Found 6 (18 requested) and removed 18 (9 requested) atoms. Cycle 8: After refmac, R = 0.1971 (Rfree = 0.000) for 2770 atoms. Found 6 (17 requested) and removed 15 (8 requested) atoms. Cycle 9: After refmac, R = 0.2011 (Rfree = 0.000) for 2756 atoms. Found 5 (17 requested) and removed 12 (8 requested) atoms. Cycle 10: After refmac, R = 0.1976 (Rfree = 0.000) for 2740 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.33 Search for helices and strands: 0 residues in 0 chains, 2835 seeds are put forward Round 1: 204 peptides, 35 chains. Longest chain 15 peptides. Score 0.424 Round 2: 226 peptides, 33 chains. Longest chain 23 peptides. Score 0.526 Round 3: 219 peptides, 30 chains. Longest chain 24 peptides. Score 0.546 Round 4: 232 peptides, 28 chains. Longest chain 28 peptides. Score 0.609 Round 5: 247 peptides, 33 chains. Longest chain 27 peptides. Score 0.588 Taking the results from Round 4 Chains 28, Residues 204, Estimated correctness of the model 18.1 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5232 reflections ( 96.71 % complete ) and 6102 restraints for refining 2885 atoms. 5189 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2222 (Rfree = 0.000) for 2885 atoms. Found 17 (18 requested) and removed 37 (9 requested) atoms. Cycle 12: After refmac, R = 0.2026 (Rfree = 0.000) for 2833 atoms. Found 13 (18 requested) and removed 17 (9 requested) atoms. Cycle 13: After refmac, R = 0.1949 (Rfree = 0.000) for 2810 atoms. Found 7 (18 requested) and removed 17 (9 requested) atoms. Cycle 14: After refmac, R = 0.1840 (Rfree = 0.000) for 2794 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.1797 (Rfree = 0.000) for 2773 atoms. Found 4 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.30 Search for helices and strands: 0 residues in 0 chains, 2849 seeds are put forward Round 1: 207 peptides, 33 chains. Longest chain 18 peptides. Score 0.464 Round 2: 227 peptides, 33 chains. Longest chain 17 peptides. Score 0.529 Round 3: 216 peptides, 28 chains. Longest chain 18 peptides. Score 0.563 Round 4: 206 peptides, 28 chains. Longest chain 26 peptides. Score 0.533 Round 5: 206 peptides, 25 chains. Longest chain 27 peptides. Score 0.574 Taking the results from Round 5 Chains 25, Residues 181, Estimated correctness of the model 4.2 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 5232 reflections ( 96.71 % complete ) and 6141 restraints for refining 2855 atoms. 5313 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2186 (Rfree = 0.000) for 2855 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 17: After refmac, R = 0.2074 (Rfree = 0.000) for 2828 atoms. Found 17 (18 requested) and removed 25 (9 requested) atoms. Cycle 18: After refmac, R = 0.1999 (Rfree = 0.000) for 2800 atoms. Found 10 (18 requested) and removed 16 (9 requested) atoms. Cycle 19: After refmac, R = 0.1954 (Rfree = 0.000) for 2786 atoms. Found 9 (17 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.1875 (Rfree = 0.000) for 2781 atoms. Found 5 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 2855 seeds are put forward Round 1: 187 peptides, 34 chains. Longest chain 13 peptides. Score 0.377 Round 2: 207 peptides, 33 chains. Longest chain 15 peptides. Score 0.464 Round 3: 213 peptides, 32 chains. Longest chain 18 peptides. Score 0.499 Round 4: 198 peptides, 32 chains. Longest chain 15 peptides. Score 0.448 Round 5: 204 peptides, 28 chains. Longest chain 22 peptides. Score 0.527 Taking the results from Round 5 Chains 28, Residues 176, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5232 reflections ( 96.71 % complete ) and 6447 restraints for refining 2928 atoms. 5657 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2325 (Rfree = 0.000) for 2928 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. Cycle 22: After refmac, R = 0.2134 (Rfree = 0.000) for 2904 atoms. Found 14 (18 requested) and removed 13 (9 requested) atoms. Cycle 23: After refmac, R = 0.2048 (Rfree = 0.000) for 2900 atoms. Found 4 (18 requested) and removed 13 (9 requested) atoms. Cycle 24: After refmac, R = 0.2019 (Rfree = 0.000) for 2890 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. Cycle 25: After refmac, R = 0.1976 (Rfree = 0.000) for 2881 atoms. Found 1 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.30 Search for helices and strands: 0 residues in 0 chains, 2952 seeds are put forward Round 1: 199 peptides, 35 chains. Longest chain 13 peptides. Score 0.406 Round 2: 198 peptides, 31 chains. Longest chain 14 peptides. Score 0.463 Round 3: 206 peptides, 31 chains. Longest chain 14 peptides. Score 0.490 Round 4: 191 peptides, 30 chains. Longest chain 15 peptides. Score 0.454 Round 5: 209 peptides, 30 chains. Longest chain 19 peptides. Score 0.514 Taking the results from Round 5 Chains 31, Residues 179, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5232 reflections ( 96.71 % complete ) and 6782 restraints for refining 3010 atoms. 5998 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2224 (Rfree = 0.000) for 3010 atoms. Found 18 (19 requested) and removed 18 (9 requested) atoms. Cycle 27: After refmac, R = 0.2024 (Rfree = 0.000) for 2991 atoms. Found 10 (19 requested) and removed 9 (9 requested) atoms. Cycle 28: After refmac, R = 0.1953 (Rfree = 0.000) for 2979 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. Cycle 29: After refmac, R = 0.1913 (Rfree = 0.000) for 2968 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.1906 (Rfree = 0.000) for 2959 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 3037 seeds are put forward Round 1: 171 peptides, 31 chains. Longest chain 12 peptides. Score 0.365 Round 2: 190 peptides, 32 chains. Longest chain 11 peptides. Score 0.420 Round 3: 192 peptides, 28 chains. Longest chain 19 peptides. Score 0.488 Round 4: 197 peptides, 30 chains. Longest chain 15 peptides. Score 0.475 Round 5: 180 peptides, 25 chains. Longest chain 17 peptides. Score 0.492 Taking the results from Round 5 Chains 25, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5232 reflections ( 96.71 % complete ) and 7176 restraints for refining 3010 atoms. 6581 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2468 (Rfree = 0.000) for 3010 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 32: After refmac, R = 0.2228 (Rfree = 0.000) for 2991 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 33: After refmac, R = 0.2111 (Rfree = 0.000) for 2982 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 34: After refmac, R = 0.2064 (Rfree = 0.000) for 2976 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 35: After refmac, R = 0.1897 (Rfree = 0.000) for 2978 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 3065 seeds are put forward Round 1: 155 peptides, 29 chains. Longest chain 20 peptides. Score 0.336 Round 2: 189 peptides, 31 chains. Longest chain 20 peptides. Score 0.432 Round 3: 187 peptides, 30 chains. Longest chain 13 peptides. Score 0.440 Round 4: 194 peptides, 30 chains. Longest chain 19 peptides. Score 0.465 Round 5: 184 peptides, 29 chains. Longest chain 17 peptides. Score 0.445 Taking the results from Round 4 Chains 30, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5232 reflections ( 96.71 % complete ) and 6838 restraints for refining 2965 atoms. 6212 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2345 (Rfree = 0.000) for 2965 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 37: After refmac, R = 0.1978 (Rfree = 0.000) for 2947 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 38: After refmac, R = 0.1934 (Rfree = 0.000) for 2942 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 39: After refmac, R = 0.1885 (Rfree = 0.000) for 2938 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 40: After refmac, R = 0.1925 (Rfree = 0.000) for 2938 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 3014 seeds are put forward Round 1: 150 peptides, 30 chains. Longest chain 12 peptides. Score 0.299 Round 2: 171 peptides, 30 chains. Longest chain 18 peptides. Score 0.382 Round 3: 168 peptides, 28 chains. Longest chain 11 peptides. Score 0.403 Round 4: 177 peptides, 27 chains. Longest chain 18 peptides. Score 0.451 Round 5: 161 peptides, 25 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 4 Chains 28, Residues 150, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5232 reflections ( 96.71 % complete ) and 6764 restraints for refining 2940 atoms. 6145 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2140 (Rfree = 0.000) for 2940 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 42: After refmac, R = 0.1948 (Rfree = 0.000) for 2931 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 43: After refmac, R = 0.1983 (Rfree = 0.000) for 2931 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 44: After refmac, R = 0.1794 (Rfree = 0.000) for 2935 atoms. Found 11 (18 requested) and removed 14 (9 requested) atoms. Cycle 45: After refmac, R = 0.1806 (Rfree = 0.000) for 2924 atoms. Found 11 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 3007 seeds are put forward Round 1: 125 peptides, 24 chains. Longest chain 10 peptides. Score 0.301 Round 2: 159 peptides, 26 chains. Longest chain 17 peptides. Score 0.402 Round 3: 156 peptides, 26 chains. Longest chain 17 peptides. Score 0.391 Round 4: 155 peptides, 24 chains. Longest chain 12 peptides. Score 0.420 Round 5: 167 peptides, 24 chains. Longest chain 20 peptides. Score 0.463 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 143, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1vjv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5232 reflections ( 96.71 % complete ) and 6722 restraints for refining 2981 atoms. 6106 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1943 (Rfree = 0.000) for 2981 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1925 (Rfree = 0.000) for 2965 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1935 (Rfree = 0.000) for 2950 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1824 (Rfree = 0.000) for 2940 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:13:49 GMT 2018 Job finished. TimeTaking 51.05 Used memory is bytes: 1839456